You can use PDFViewCtrl.
GetAnnotationCanvas to get a Canvas that you can put objects onto.
There are also some associated methods for getting the scroll positions of this canvas, in particular PDFViewCtrl.
GetAnnotationCanvasHorizontalOffset Instead of using your own layer, most likely you can reuse the annotation canvas for your task.
If not, please elaborate on what you are trying to accomplish (screen shots help a lot)